LineagePulse

Lineage 1

Percentage of genes called significant as we change q-value threshold

## 62.2% of the genes are called significant when we require the adjusted p-value to be smaller than 0.01

Heatmap of significant genes

Scaled log expression of lineage 1. Heatmap of top 500 significant genes detected by three methods.

Log expression of lineage 1. Heatmap of top 500 significant genes detected by three methods.

Visualization of 9 most significant genes

Visualization of 9 least significant genes

Venn Diagram

Lineage 2

Percentage of genes called significant as we change q-value threshold

## 76.16% of the genes are called significant when we require the adjusted p-value to be smaller than 0.01

Heatmap of significant genes

Scaled log expression of lineage 2. Heatmap of top 500 significant genes detected by three methods.

Log expression of lineage 2. Heatmap of top 500 significant genes detected by three methods.

Visualization of 9 most significant genes

Visualization of 9 least significant genes

Venn Diagram

Observation

• Most of the genes (~70%) are called significant under a commonly used significant level 0.01.
• LineagePulse works well in detecting time-varying genes. However, it is very sensitive to outliers: several of the most significant genes are detected simply due to outliers (?) as shown in the heatmap.